diff --git a/modules/seq/alg/src/merge_pairwise_alignments.cc b/modules/seq/alg/src/merge_pairwise_alignments.cc
index 664f6ccc6315da166fd169daa20951d4f1b32367..35126c2bdc0d3acbf6d2a0cd21a52325822db1fc 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.cc
+++ b/modules/seq/alg/src/merge_pairwise_alignments.cc
@@ -89,7 +89,7 @@ SequenceHandle shift_reference(const SequenceHandle& ref_seq,
                                             new_sequence.str());
   if (ref_seq.HasAttachedView())
     s.AttachView(ref_seq.GetAttachedView());
-  s.SetSequenceOffset(s.GetSequenceOffset());
+  s.SetOffset(s.GetOffset());
   return s;
 }
 
@@ -123,7 +123,7 @@ SequenceHandle realign_sequence(const AlignmentHandle& aln,
   SequenceHandle s=CreateSequence(s2.GetName(), new_sequence.str());
   if (s2.HasAttachedView())
     s.AttachView(s2.GetAttachedView());
-  s.SetSequenceOffset(s2.GetSequenceOffset());
+  s.SetOffset(s2.GetOffset());
   return s;
 }  
 
diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index 9d6e8d213f743a6383d4cdaf2a2eaee2a7f132c5..243ec0d49108938923169456f4ba9e9cef8a927f 100644
--- a/modules/seq/base/doc/seq.rst
+++ b/modules/seq/base/doc/seq.rst
@@ -148,15 +148,15 @@ The SequenceHandle
     Returns the name of the sequence. Also available as the property
     :attr:`name`
   
-  .. method:: SetSequenceOffset()
+  .. method:: SetOffset()
   
     Set the :ref:`sequence offset <sequence-offset>`. By default, the offset is
-    0. Also available as the property :attr:`sequence_offset`.
+    0. Also available as the property :attr:`offset`.
     
-  .. method:: GetSequenceOffset()
+  .. method:: GetOffset()
     
     Returns the :ref:`sequence offset <sequence-offset>`. Also available as
-    :attr:`sequence_offset`.
+    :attr:`offset`.
     
     
   .. method:: GetGaplessString()
@@ -181,7 +181,7 @@ The SequenceHandle
   
     Shorthand for :meth:`GetAttachedView`.
 
-  .. attribute:: sequence_offset
+  .. attribute:: offset
   
     Shorthand for :meth:`GetSequenceOffset`/:meth:`SetSequenceOffset`
 
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index c88fe7f27dc5d8e88d5c4eabaa706b1dc66ba210..28543e04d50d5375b102ab67474d96978a912c0e 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -209,7 +209,7 @@ void const_seq_handle_def(O& bp_class)
     .def("GetResidue", &C::GetResidue)
     .def("GetOneLetterCode", &C::GetOneLetterCode)
     .def("__getitem__", &C::GetOneLetterCode)
-    .def("GetSequenceOffset", &C::GetSequenceOffset)
+    .def("GetOffset", &C::GetOffset)
     .def("Copy", &C::Copy)
     .def("IsValid", &C::IsValid)
     .def("GetFirstNonGap", &C::GetFirstNonGap)
@@ -229,7 +229,7 @@ void const_seq_handle_def(O& bp_class)
     .add_property("name",
                   make_function(&C::GetName,
                                 return_value_policy<copy_const_reference>()))
-    .add_property("sequence_offset", &C::GetSequenceOffset)
+    .add_property("offset", &C::GetOffset)
     .add_property("gapless_string", &C::GetGaplessString)
     .add_property("string",
                   make_function(&C::GetString,
@@ -252,7 +252,7 @@ void export_sequence()
   seq_handle
     .def("__setitem__", &SequenceHandle::SetOneLetterCode)
     .def("SetOneLetterCode", &SequenceHandle::SetOneLetterCode)  
-    .def("SetSequenceOffset", &SequenceHandle::SetSequenceOffset)
+    .def("SetOffset", &SequenceHandle::SetOffset)
     .def("AttachView", attach_one)
     .def("AttachView", attach_two)
     .def("SetString", &SequenceHandle::SetString)
@@ -265,8 +265,8 @@ void export_sequence()
                   make_function(&SequenceHandle::GetName,
                                 return_value_policy<copy_const_reference>()),
                   &SequenceHandle::SetName)
-    .add_property("sequence_offset", &SequenceHandle::GetSequenceOffset,
-                  &SequenceHandle::SetSequenceOffset)
+    .add_property("offset", &SequenceHandle::GetOffset,
+                  &SequenceHandle::SetOffset)
   ;
 
   implicitly_convertible<SequenceHandle, ConstSequenceHandle>();
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index edc54340b7d4a4ea017035465f7c5c468c53b302..d2a7ab85d387051d43edbadac9419925b5ac7fee 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -255,12 +255,12 @@ void AlignmentHandle::SetSequenceName(int seq_index, const String& name)
 void AlignmentHandle::SetSequenceOffset(int seq_index, int offset)
 {
   this->CheckValidity();
-  impl_->GetSequence(seq_index)->SetSequenceOffset(offset);
+  impl_->GetSequence(seq_index)->SetOffset(offset);
 }
 
 int AlignmentHandle::GetSequenceOffset(int seq_index)
 {
   this->CheckValidity();
-  return impl_->GetSequence(seq_index)->GetSequenceOffset();
+  return impl_->GetSequence(seq_index)->GetOffset();
 }
 }}
diff --git a/modules/seq/base/src/impl/sequence_impl.cc b/modules/seq/base/src/impl/sequence_impl.cc
index 64a1c8cc5c1e60aebdf5cd9fdd15eedb12986d40..a99ea9b6389bcc2655db1bdc459ce6e243253aa7 100644
--- a/modules/seq/base/src/impl/sequence_impl.cc
+++ b/modules/seq/base/src/impl/sequence_impl.cc
@@ -74,7 +74,7 @@ void SequenceImpl::SetString(const String& seq)
 
 SequenceImpl::SequenceImpl(const String& seq_name,
                    const String& seq_string)
-  : seq_name_(seq_name), seq_string_(seq_string), sequence_offset_(0)
+  : seq_name_(seq_name), seq_string_(seq_string), offset_(0)
 {
   this->ShiftsFromSequence();
 }
@@ -82,7 +82,7 @@ SequenceImpl::SequenceImpl(const String& seq_name,
 SequenceImplPtr SequenceImpl::Copy() const
 {
   SequenceImplPtr new_seq(new SequenceImpl(seq_name_, seq_string_));
-  new_seq->sequence_offset_=sequence_offset_;
+  new_seq->offset_=offset_;
   new_seq->shifts_=shifts_;
   new_seq->attached_view_=attached_view_;
   return new_seq;
@@ -139,7 +139,7 @@ int SequenceImpl::GetResidueIndex(int pos) const
     if (s.start<=pos)
       shift+=s.shift;
   }
-  return pos-shift+sequence_offset_;
+  return pos-shift+offset_;
 }
 
 void SequenceImpl::SetName(const String& seq_name)
@@ -154,7 +154,7 @@ const String& SequenceImpl::GetName() const
 
 int SequenceImpl::GetPos(int index) const
 {
-  int shifted_index=index-sequence_offset_;
+  int shifted_index=index-offset_;
   int pos=this->GetPosNoBounds(shifted_index);
   if (pos<0 || pos>=static_cast<int>(seq_string_.length()))
     throw Error("number not covered in sequence");
@@ -174,15 +174,15 @@ int SequenceImpl::GetPosNoBounds(int index) const
 }
 
 /// \brief  Set offset for sequence alignment.
-void SequenceImpl::SetSequenceOffset(int offset)
+void SequenceImpl::SetOffset(int offset)
 {
-  sequence_offset_=offset;
+  offset_=offset;
 }
 
 /// \brief Get sequence offset
-int SequenceImpl::GetSequenceOffset() const
+int SequenceImpl::GetOffset() const
 {
-  return sequence_offset_;
+  return offset_;
 }
 
 int SequenceImpl::GetLength() const {
@@ -259,7 +259,7 @@ void SequenceImplToInfo(const SequenceImplPtr& sequence, info::InfoGroup& group)
   group.SetTextData(sequence->GetString());
   group.SetAttribute("name", sequence->GetName());
   std::ostringstream ss;
-  ss << sequence->GetSequenceOffset();
+  ss << sequence->GetOffset();
   group.SetAttribute("offset", ss.str());
 }
 
@@ -271,7 +271,7 @@ SequenceImplPtr SequenceImplFromInfo(const info::InfoGroup& group)
   ss >> offset;
   SequenceImplPtr sequence=SequenceImpl::FromString(group.GetAttribute("name"), 
                                                     text);
-  sequence->SetSequenceOffset(offset);
+  sequence->SetOffset(offset);
   return sequence;
 }
 
diff --git a/modules/seq/base/src/impl/sequence_impl.hh b/modules/seq/base/src/impl/sequence_impl.hh
index f7d1110c98a0bbb315ceaf4e3b2d7f5c925a547c..f89b3c4bf8f939a7b03b2c20f4ccaf37e34d8edf 100644
--- a/modules/seq/base/src/impl/sequence_impl.hh
+++ b/modules/seq/base/src/impl/sequence_impl.hh
@@ -85,15 +85,15 @@ public:
 
   /// \brief Get sequence offset from N-terminus
   ///
-  /// \sa #SetSequenceOffset
-  int GetSequenceOffset() const;
+  /// \sa #SetOffset
+  int GetOffset() const;
 
   /// \brief Set sequence offset
   ///
   /// By default the sequence offset is zero, i.e. the beginning of the sequence
   /// lies exactly at the N-terminus. Setting the sequence offset to a positive
   /// number will shift the sequence towards the C-terminus.
-  void SetSequenceOffset(int offset);
+  void SetOffset(int offset);
 
   /// \brief Get lenght of sequence, including gaps.
   int GetLength() const;
@@ -155,7 +155,7 @@ private:
   String              seq_string_;
   std::list<Shift>    shifts_;
   bool                editing_;
-  int                 sequence_offset_;
+  int                 offset_;
   mol::EntityView          attached_view_;
 };
 
diff --git a/modules/seq/base/src/sequence_handle.cc b/modules/seq/base/src/sequence_handle.cc
index 8bf31de26f6cb75396e27f3a61f3c3e6eaa32eae..13063990d6f093947354436e4cc619c546c36639 100644
--- a/modules/seq/base/src/sequence_handle.cc
+++ b/modules/seq/base/src/sequence_handle.cc
@@ -88,10 +88,10 @@ String ConstSequenceHandle::GetGaplessString() const
   return Impl()->GetGaplessString();
 }
 
-int ConstSequenceHandle::GetSequenceOffset() const
+int ConstSequenceHandle::GetOffset() const
 {
   this->CheckValidity();
-  return Impl()->GetSequenceOffset();  
+  return Impl()->GetOffset();  
 }
 
 
@@ -183,10 +183,10 @@ void SequenceHandle::SetString(const String& seq)
   return Impl()->SetString(seq);   
 }
 
-void SequenceHandle::SetSequenceOffset(int offset)
+void SequenceHandle::SetOffset(int offset)
 {
   this->CheckValidity();
-  return Impl()->SetSequenceOffset(offset);   
+  return Impl()->SetOffset(offset);   
 }
 
 
@@ -268,10 +268,10 @@ String SequenceHandle::GetGaplessString() const
   return Impl()->GetGaplessString();
 }
 
-int SequenceHandle::GetSequenceOffset() const
+int SequenceHandle::GetOffset() const
 {
   this->CheckValidity();
-  return Impl()->GetSequenceOffset();  
+  return Impl()->GetOffset();  
 }
 
 SequenceHandle::operator ConstSequenceHandle() const
diff --git a/modules/seq/base/src/sequence_handle.hh b/modules/seq/base/src/sequence_handle.hh
index 46004d0a85502c59930652f2d8ea80142cf1e61d..923dec13f217105a13205f334aec02ed5d7289ab 100644
--- a/modules/seq/base/src/sequence_handle.hh
+++ b/modules/seq/base/src/sequence_handle.hh
@@ -84,8 +84,8 @@ public:
 
   /// \brief Get sequence offset from N-terminus
   ///
-  /// \sa SequenceHandle::SetSequenceOffset
-  int GetSequenceOffset() const;  
+  /// \sa SequenceHandle::SetOffset
+  int GetOffset() const;  
   
   /// \brief Get lenght of sequence, including gaps.
   int GetLength() const;
@@ -140,7 +140,7 @@ private:
 /// "multiple sequence alignment". The class allows for fast mapping between
 /// residue index and position in the sequence. The GetResidueIndex() method
 /// maps from position in the sequence to residue index, taking the
-/// \ref GetSequenceOffset() "sequence offset" into account. The reverse
+/// \ref GetOffset() "sequence offset" into account. The reverse
 /// mapping is done with GetPos().
 /// 
 /// Optionally, an entity view may be attached to the sequence with
@@ -195,8 +195,8 @@ public:
 
   /// \brief Get sequence offset from N-terminus
   ///
-  /// \sa SequenceHandle::SetSequenceOffset
-  int GetSequenceOffset() const;  
+  /// \sa SequenceHandle::GetOffset
+  int GetOffset() const;  
   
   /// \brief Get lenght of sequence, including gaps.
   int GetLength() const;
@@ -246,7 +246,7 @@ public:
   /// By default the sequence offset is zero, i.e. the beginning of the sequence
   /// lies exactly at the N-terminus. Setting the sequence offset to a positive
   /// number will shift the sequence towards the C-terminus.
-  void SetSequenceOffset(int offset);
+  void SetOffset(int offset);
 
   /// \brief attach entity view to sequence
   ///
diff --git a/modules/seq/base/src/views_from_sequences.cc b/modules/seq/base/src/views_from_sequences.cc
index 7ab0ff1f6806c1d303baac5e0689f12d06d91f89..dad47106b659bb034f577533333019d2e8653258 100644
--- a/modules/seq/base/src/views_from_sequences.cc
+++ b/modules/seq/base/src/views_from_sequences.cc
@@ -66,9 +66,9 @@ ViewsFromSequences(const ConstSequenceHandle& seq1,
   mol::ResidueViewList res_b=src_b.GetResidueList();  
   int pos=0, index_a=0, index_b=0;
   while (skip_gaps(seq1, seq2, pos, index_a, index_b)) {
-    dst_a.AddResidue(res_a.at(seq1.GetSequenceOffset()+index_a), 
+    dst_a.AddResidue(res_a.at(seq1.GetOffset()+index_a), 
                      mol::ViewAddFlag::INCLUDE_ATOMS);
-    dst_b.AddResidue(res_b.at(seq2.GetSequenceOffset()+index_b), 
+    dst_b.AddResidue(res_b.at(seq2.GetOffset()+index_b), 
                      mol::ViewAddFlag::INCLUDE_ATOMS);
     pos+=1;
     index_a+=1;
diff --git a/modules/seq/base/tests/test_seq.py b/modules/seq/base/tests/test_seq.py
index 4eed73b1132f82109cc0250807561cb0675db3c0..26abba6896e53f32f19ef43cb4d44e5999bb6c2f 100644
--- a/modules/seq/base/tests/test_seq.py
+++ b/modules/seq/base/tests/test_seq.py
@@ -113,9 +113,9 @@ class TestSeq(unittest.TestCase):
   def testViewsFromSequences_09(self):
     seq_a=seq.CreateSequence("A", "B-D-FGH")
     seq_a.AttachView(self.ent.Select('rname=A,B,D,F,G,H'))
-    seq_a.SetSequenceOffset(1)
+    seq_a.offset=1
     seq_b=seq.CreateSequence("B", "B-DEF-H")
-    seq_b.SetSequenceOffset(1)
+    seq_b.offset=1
     seq_b.AttachView(self.ent.Select('rname=A,B,D,E,F,H'))
     a, b=seq.ViewsFromSequences(seq_a, seq_b)
     string_a=''.join([r.one_letter_code for r in a.residues])
diff --git a/modules/seq/base/tests/test_sequence.cc b/modules/seq/base/tests/test_sequence.cc
index 21c588a46cfb851b46972eaa26bceced3e55a8d4..e787aafb7c3de95e8d93c2b55de8b3b9bba7c8f4 100644
--- a/modules/seq/base/tests/test_sequence.cc
+++ b/modules/seq/base/tests/test_sequence.cc
@@ -136,7 +136,7 @@ BOOST_AUTO_TEST_CASE(seq_offset)
 {
   SequenceHandle s=CreateSequence("S1", "-afc--de-f");
   SequenceHandle s2=CreateSequence("S1", "-afc--de-f");
-  s.SetSequenceOffset(2);
+  s.SetOffset(2);
   BOOST_CHECK_THROW(s.GetPos(-1), Error);
   BOOST_CHECK_THROW(s.GetPos(0), Error);
   BOOST_CHECK_THROW(s.GetPos(1), Error);
@@ -155,7 +155,7 @@ BOOST_AUTO_TEST_CASE(seq_offset)
   BOOST_CHECK_THROW(s.GetResidueIndex(10), std::out_of_range);
   BOOST_CHECK_THROW(s.GetResidueIndex(-1), std::out_of_range);
 
-  s.SetSequenceOffset(-1);
+  s.SetOffset(-1);
   BOOST_CHECK_THROW(s.GetPos(-2), Error);
   BOOST_CHECK_EQUAL(s.GetPos(-1), 1);
   BOOST_CHECK_EQUAL(s.GetPos(0), 2);